Friction is a familiar phenomenon to humankind and has long been studied; however, it is fundamentally difficult to understand because of the complex processes that contribute to it. For elucidating friction, it is helpful to simplify the system. In this respect, molecular manipulation, in which a single molecule or atom on a surface is moved by the tip of a scanning probe microscope, is an ideal research target. In this paper, we combine noncontact atomic force microscopy, inelastic electron tunneling spectroscopy, and density functional theory calculations to investigate the molecular manipulation process of a single CO molecule on Cu(110) and Cu(111) surfaces at low temperature. We discovered the presence of a metastable adsorption site that is not occupied when the tip is far from the surface but is engaged for close tip positions. This adsorption site plays the role of an intermediate state in the reaction path of manipulation, and this intermediate is important for understanding the dynamics of manipulation and dynamic friction. We elaborate the process leading to the above conclusions in detail and discuss future perspectives.